[gmx-users] unwrap trajectory file using -pbc nojump

[Tsjerk Wassenaar]

Hi Yutian Yang,

I don't think it's because of the size of the system. Can you run trjconv
without -pbc nojump? And did you check the trajectory with gmxcheck? Does
the output file  exceed a maximum file size limit?

Hope it helps,

Tsjerk


On Wed, Jul 3, 2013 at 9:22 PM, Yutian Yang <yyang18 at syr.edu> wrote:

> Dear all,
>
> I want to remove PBC effects for my system and calculate the diffusion
> coefficient. I am using Gromacs 4.5.4. My system is a 15 nm cubic box with
> 376 polymer chains each with 28 beads. The simulation time is about 2000
> ns. However, when I use the command
>
> trjconv_mpi -f all.xtc -s polyeqm.gro -o allnojump.xtc -pbc nojump
>
> The program stops at around 500 ns. It doesn't get killed, nor proceeds,
> but stuck there and I have to manually cease the program. I have tried
> different systems with same attributes, all with the same problem. Is it
> because it is a large system that makes the program running out of memory?
>
> Thank you!
>
> Yutian
>
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-- 
Tsjerk A. Wassenaar, Ph.D.